Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Premise of Study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated ten transcriptomes and incorporated existing RNA-seq data to infer a multi-locus nuclear phylogeny of the Cypripedioideae and to determine if a whole genome duplication event (WGD) correlated to the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families.
Methods: Transcriptome data was used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree.
Key results: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny.
Conclusions: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.

研究背景：兜兰亚科（Cypripedioideae）是兰科（Orchidaceae）中形态学特征独特的亚科，同时也是兰科中基因组规模最大的类群之一，其大基因组的成因可能与多倍化或其他基因组进化机制相关。本研究构建了10个转录组（transcriptome）并整合已公开的RNA测序（RNA-seq）数据，旨在推断兜兰亚科的多位点核基因系统发育关系，并探究全基因组复制（whole genome duplication, WGD）事件是否与该亚科的大基因组规模存在关联。深入解析古多倍化事件的发生时序，有助于理解这个物种最丰富的植物类群之一的进化历程。
研究方法：利用转录组数据鉴定低拷贝直系同源基因，以推断兰科的系统发育关系；同时鉴定旁系同源基因，从而将全基因组复制事件锚定至物种树的对应分支。
主要结果：本研究基于转录组的系统发育分析验证了过往仅使用少量分子标记但涵盖更多类群的相关研究所得出的类群亲缘关系。未在兜兰亚科的基部支系检测到全基因组复制事件，但在兰科的茎干支系上鉴定到一例全基因组复制事件。同时验证了此前在单子叶植物（monocot）更深层级系统发育中被报道的全基因组复制事件。
研究结论：尽管全基因组复制在兰科的进化历程中发挥了一定作用，但多倍化并非导致兜兰亚科基因组规模庞大的原因。本研究鉴定得到的775个高度保守的单拷贝核基因集，将为未来兰科进化相关研究提供重要的研究资源。